Bio: : NEXUS: a Perl API for the NEXUS format for comparative biological data. - Thomas Hladish; Vivek Gopalan; Chengzhi Liang; Wei-Gang Qiu; Peter Yang; Arlin Stoltzfus (BMC Bioinform., 2007)

EpiFire: An open source C++ library and application for contact network epidemiology. - Thomas Hladish; Eugene Melamud; Luis Barrera; Alison P. Galvani; Lauren Ancel Meyers (BMC Bioinform., 2012)

Evaluating targeted COVID-19 vaccination strategies with agent-based modeling. - Thomas Hladish; Alexander N. Pillai; Carl A. B. Pearson; Kok Ben Toh; Andrea C. Tamayo; Arlin Stoltzfus; Ira M. Longini (PLoS Comput. Biol., 2024)